This is something I struggled with for a long time...then I wrote my own tools, which started out a few years ago simply as mental ray shaders that blended multiple projections together based on painted mattes, geometry occlusion, facing ratio, etc. The tools progressed over the years to include a UI that minimized the iterative tasks of setting up the shading networks, and extended the capabilities of Maya's viewport feedback (among other things.)

I released the tools as a plugin suite under the name the Mattepainting Toolkit for Maya, which you can find here:

Though the tools aren't free, the most recent release from a couple weeks ago has an OpenGL layering feature that allows for the projections to be layered and blended (with embedded alphas) directly in Maya's viewport. There's a demo available on the site that is fully-functional (with the exception of watermarks), which should give you an idea of how the tools can help you with a multiple projection workflow. Here's a screen capture that shows the viewport layering in action: